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At the beginning of the stage, there is a cutscene which shows two R.O.B.s activating a Subspace Bomb. They hang their heads in sadness as it detonates. From atop the castle, Marth sees the explosion and seems shocked by it. Soon afterwards, an army of Primids approaches the castle. Marth raises Falchion and prepares to defend the castle. After defeating the foes and leaving the castle, Marth stares at the sphere of Subspace caused by the earlier explosion, when Meta Knight appears out of nowhere and attacks Marth. After an evenly matched sword duel, each one sees Primids over their rival's shoulder. They dodge around each other and destroy the Primids with their swords. They turn to face each other, surprised to realize they have a common enemy. After more Primids surround them, they team up to destroy them.

After another level that involves destroying more enemies, Meta Knight and Marth see the Ancient Minister carrying another Subspace Bomb. They both attempt to destroy it, but fail. Suddenly, the yell, "Great Aether!!" is heard, and Ike appears, using his trademark Aether to slice through the Subspace Bomb, destroying it. Marth, Meta Knight, and Ike all then team up to take on more enemies from Subspace. After defeating the enemies, the stage is cleared, and the three swordsmen are added to the player's party. The final cutscene involves the swordsmen chasing after the Ancient Minister, who was able to escape.

After the level is complete, an entirely different cutscene proceeds in the depths of The Lake Shore, in which Luigi is seen timidly confronting a Waddle Dee. When the harmless creature naturally avoids confrontation, Luigi is relived but shocked by the appearance of another Waddle Dee. But as he prepares to "fight", King Dedede appears behind him and ambushes him with his mallet; turning him into a trophy. King Dedede then notices Wario and his cargo containing the trophies of Peach/Zelda and Ness approaching, and hides. Using the Luigi trophy as bait, King Dedede is able to steal the cargo and the trophies, much to the chagrin of Wario.